Anvilicious: Being an "eco-goth" band, the song "Earth, Wind, Fire, and Air" is thick on its message on the importance of being environmentally friendly. It's still very catchy nevertheless.
Awesome Music: While Zombie Island delved into the punk genre, Witch's Ghost delved into gothic-themed Grunge with the Hex Girls. They provide some of the best music of the movie. Not as great as Zombie Island's music, but it's still great nonetheless.
Scooby and Shaggy successfully tailing the mayor and evading detection. At one point they do a Fakeout Makeout when he gets suspicious.
The Reveal that Ben was Evil All Along doubles as this and as Nightmare Fuel. He then takes the book, makes the huge announcement, calls out the Mayor and Thorn's dad for using Sarah's image horribly, and starts doing magic. Scary? Yes. Awesome? Hell yes.
When the Scooby Gang realizes that Ben was evil and used them to get Sarah's book of witchcraft, they immediately use their brains to steal the book from him for as long as they can. This results in their best display of teamwork and Character Development compared to Zombie Island, where they nearly got killed.
Also though it fails, Shaggy plucking up his courage to douse Sarah with water, hoping it would melt her like in The Wizard of Oz. Especially considering this is Shaggy.
Also the entire gang playing Keep Away with the book as Sarah's magic incapacitates them long enough for Thorn to get the book and read it.
Ensemble Darkhorse: The Hex Girls proved to be very popular and have become recurring characters in the franchise ever since.
As noted under Artistic License – Religion, Thorn being 1/16th Wiccan is complete nonsense. However she still clearly practices some elements of Wicca which arguably still makes her the best chance to defeat Sarah.
Also, Ben Ravencroft first heard about Mystery Inc from their solving the mystery of the "Moat Monster". The Moat Monster was the same story that Daphne brought up in her interview towards the beginning of Zombie Island, which means 'The Witch's Ghost' takes place in the same universe as 'Zombie Island'. However, Fridge Logic arises when you realize that Ravencroft wouldn't have waited however many years between Mystery Inc's initial retirement and their eventual revival just to get that specific team of kids to help him. After all, what would Ravencroft have done if the gang never got back together?
Daphne and Fred still operated as mystery-solvers; that is what inspired Fred to get the team back together in Zombie Island. And they were public about it, including Daphne having her own show. All Ravencroft would have needed was to keep a watch on them, and continue his own searches in the meantime. Additionally, we could assume that he did enlist the "help" of other mystery-solving gangs...if we also assume that there are in fact other mystery-solving gangs.
The two guards dressed as undead barbarians are unsettling.
The Hex Girls' first appearance is intentionally a bit creepy.
The attacks from the fake Witch's Ghost.
The sleuthing scenes are much creepier and quiet than usual here.
Ben is elated to finally find Sarah's book, which will finally prove that his ancestor was a peaceful, kind Wiccan and not a witch... only the book has a massive, scary skull on it. And we get a deep Scare Chord as we realize Ben was not telling the truth.
Ben testing his powers and summoning Sarah are epic and terrifying. Sarah may have only been introduced in this movie, and only just been established as evil, but you will be on edge and horrified as Ben summons her. "THIS IS EVIL'S FINEST HOUR"!
The evil pumpkins being sent after the gang. One of them grabs onto Daphne with a vine and is squealing as it prepares to eat her. And their deaths are pretty scary as well, being crushed and seemingly still being alive after breaking into pieces and puddles.
Though Played for Laughs, when the giant turkey wakes to see what he believes are two pilgrims about to kill and eat him, he understandably screams and runs for his life.
Sarah's defeat as she drags her descendant Ben screaming into the hellish netherworld she'd been trapped in for centuries. Thankfully, the book is burned, dooming the Ravencrofts to never return.
The ending song, "The Witch's Ghost", is pretty creepy and epic as befitting the credits of a pretty dark and scary Scooby film.